Barker David L, Hansen Mark S T, Faruqi A Fawad, Giannola Diane, Irsula Orlando R, Lasken Roger S, Latterich Martin, Makarov Vladimir, Oliphant Arnold, Pinter Jonathon H, Shen Richard, Sleptsova Irina, Ziehler William, Lai Eric
Illumina, Inc., San Diego, California 92121, USA.
Genome Res. 2004 May;14(5):901-7. doi: 10.1101/gr.1949704.
Comprehensive genome scans involving many thousands of SNP assays will require significant amounts of genomic DNA from each sample. We report two successful methods for amplifying whole-genomic DNA prior to SNP analysis, multiple displacement amplification, and OmniPlex technology. We determined the coverage of amplification by analyzing a SNP linkage marker set that contained 2320 SNP markers spread across the genome at an average distance of 2.5 cM. We observed a concordance of >99.8% in genotyping results from genomic DNA and amplified DNA, strongly indicating the ability of both methods used to amplify genomic DNA in a highly representative manner. Furthermore, we were able to achieve a SNP call rate of >98% in both genomic and amplified DNA. The combination of whole-genome amplification and comprehensive SNP linkage analysis offers new opportunities for genetic analysis in clinical trials, disease association studies, and archiving of DNA samples.
涉及数千个单核苷酸多态性(SNP)检测的全基因组扫描需要从每个样本中获取大量的基因组DNA。我们报告了两种在SNP分析之前扩增全基因组DNA的成功方法,即多重置换扩增和全基因组多重恒温扩增技术(OmniPlex技术)。我们通过分析一个SNP连锁标记集来确定扩增的覆盖范围,该标记集包含2320个SNP标记,平均间距为2.5厘摩,分布于整个基因组。我们观察到基因组DNA和扩增DNA进行基因分型的结果一致性超过99.8%,这有力地表明了所使用的两种方法都能够以高度代表性的方式扩增基因组DNA。此外,我们在基因组DNA和扩增DNA中均实现了超过98%的SNP检出率。全基因组扩增与全面的SNP连锁分析相结合,为临床试验、疾病关联研究和DNA样本存档中的遗传分析提供了新的机遇。